Lars Kaderali
| Snapshot Date: 2021-05-05 14:51:38 -0400 (Wed, 05 May 2021) |
| URL: https://git.bioconductor.org/packages/RNAither |
| Branch: RELEASE_3_12 |
| Last Commit: c2ad330 |
| Last Changed Date: 2020-10-27 10:34:29 -0400 (Tue, 27 Oct 2020) |
| Back to Multiple platform build/check report for BioC 3.12 |
|
This page was generated on 2021-05-06 12:28:52 -0400 (Thu, 06 May 2021).
|
To the developers/maintainers of the RNAither package: Please make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 1548/1974 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| RNAither 2.38.0 (landing page) Lars Kaderali
| malbec1 | Linux (Ubuntu 18.04.5 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | | ||||||||
| merida1 | macOS 10.14.6 Mojave / x86_64 | OK | OK | WARNINGS | OK | | ||||||||
| Package: RNAither |
| Version: 2.38.0 |
| Command: /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:RNAither.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings RNAither_2.38.0.tar.gz |
| StartedAt: 2021-05-06 05:21:05 -0400 (Thu, 06 May 2021) |
| EndedAt: 2021-05-06 05:25:08 -0400 (Thu, 06 May 2021) |
| EllapsedTime: 243.1 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: RNAither.Rcheck |
| Warnings: 1 |
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### Running command:
###
### /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:RNAither.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings RNAither_2.38.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.12-bioc/meat/RNAither.Rcheck’
* using R version 4.0.5 (2021-03-31)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘RNAither/DESCRIPTION’ ... OK
* this is package ‘RNAither’ version ‘2.38.0’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘RNAither’ can be installed ... WARNING
Found the following significant warnings:
Warning: Package 'prada' is deprecated and will be removed from Bioconductor
See ‘/home/biocbuild/bbs-3.12-bioc/meat/RNAither.Rcheck/00install.out’ for details.
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... NOTE
Found the following CITATION file in a non-standard place:
inst/extdata/CITATION
Most likely ‘inst/CITATION’ should be used instead.
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... NOTE
Package in Depends field not imported from: ‘RankProd’
These packages need to be imported from (in the NAMESPACE file)
for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
PlotSpatialDistrib: no visible global function definition for
‘brewer.pal’
RankProduct: no visible global function definition for ‘RP’
compareReplicateSD: no visible global function definition for
‘brewer.pal’
compareReplicateSDPerScreen: no visible global function definition for
‘brewer.pal’
spatialDistrib: no visible global function definition for ‘brewer.pal’
Undefined global functions or variables:
RP brewer.pal
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
mainAnalysis 14.192 0.224 14.493
rnaither 7.932 0.036 7.981
gseaAnalysis 7.380 0.108 10.567
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 1 WARNING, 3 NOTEs
See
‘/home/biocbuild/bbs-3.12-bioc/meat/RNAither.Rcheck/00check.log’
for details.
RNAither.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD INSTALL RNAither ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.12-bioc/R/library’ * installing *source* package ‘RNAither’ ... ** using staged installation ** R ** data ** inst ** byte-compile and prepare package for lazy loading groupGOTerms: GOBPTerm, GOMFTerm, GOCCTerm environments built. Warning message: Package 'prada' is deprecated and will be removed from Bioconductor version 3.13 ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location groupGOTerms: GOBPTerm, GOMFTerm, GOCCTerm environments built. Warning: Package 'prada' is deprecated and will be removed from Bioconductor version 3.13 ** testing if installed package can be loaded from final location groupGOTerms: GOBPTerm, GOMFTerm, GOCCTerm environments built. Warning: Package 'prada' is deprecated and will be removed from Bioconductor version 3.13 ** testing if installed package keeps a record of temporary installation path * DONE (RNAither)
RNAither.Rcheck/RNAither-Ex.timings
| name | user | system | elapsed | |
| BScore | 0.036 | 0.004 | 0.039 | |
| DRQualControl | 0.040 | 0.000 | 0.042 | |
| LiWongRank | 0.092 | 0.000 | 0.092 | |
| MannWhitney | 0.028 | 0.000 | 0.032 | |
| RankProduct | 0.136 | 0.000 | 0.138 | |
| SNRQualControl | 0.048 | 0.000 | 0.045 | |
| Ttest | 0.028 | 0.000 | 0.026 | |
| ZPRIMEQualControl | 0.048 | 0.000 | 0.049 | |
| ZScore | 0.008 | 0.000 | 0.007 | |
| ZScorePerScreen | 0.004 | 0.000 | 0.005 | |
| ZScorePlot | 0.036 | 0.000 | 0.035 | |
| ZScorePlotTwo | 0.020 | 0.000 | 0.018 | |
| channelPlot | 0.020 | 0.000 | 0.023 | |
| closestToZero | 0.000 | 0.000 | 0.002 | |
| compareHits | 0.028 | 0.000 | 0.026 | |
| compareReplicaPlates | 0.012 | 0.000 | 0.011 | |
| compareReplicateSD | 0.108 | 0.000 | 0.110 | |
| compareReplicateSDPerScreen | 0.136 | 0.004 | 0.137 | |
| compareReplicates | 0.076 | 0.000 | 0.077 | |
| controlDensity | 0.036 | 0.000 | 0.036 | |
| controlDensityPerPlate | 0.100 | 0.004 | 0.104 | |
| controlDensityPerScreen | 0.044 | 0.000 | 0.045 | |
| controlNorm | 0.008 | 0.000 | 0.006 | |
| createSubset | 0.000 | 0.000 | 0.001 | |
| discardLabtek | 0.004 | 0.000 | 0.002 | |
| discardWells | 0.000 | 0.000 | 0.002 | |
| divNorm | 0.004 | 0.000 | 0.007 | |
| divideChannels | 0.000 | 0.000 | 0.001 | |
| eraseDataSetColumn | 0.004 | 0.000 | 0.005 | |
| findReplicates | 0.000 | 0.000 | 0.002 | |
| furthestFromZero | 0.004 | 0.000 | 0.002 | |
| generateDatasetFile | 0.008 | 0.000 | 0.008 | |
| generateRepMatNoFilter | 0.004 | 0.000 | 0.002 | |
| generateReplicateMat | 0.004 | 0.000 | 0.005 | |
| gseaAnalysis | 7.380 | 0.108 | 10.567 | |
| hitselectionPval | 0.024 | 0.000 | 0.027 | |
| hitselectionZscore | 0.016 | 0.000 | 0.015 | |
| hitselectionZscorePval | 0.016 | 0.000 | 0.014 | |
| incorporatepValVec | 0.012 | 0.000 | 0.009 | |
| indexSubset | 0.000 | 0.000 | 0.002 | |
| joinDatasetFiles | 0.008 | 0.004 | 0.011 | |
| joinDatasets | 0.004 | 0.000 | 0.002 | |
| lowessNorm | 0.004 | 0.004 | 0.006 | |
| mainAnalysis | 14.192 | 0.224 | 14.493 | |
| makeBoxplot4PlateType | 0.028 | 0.000 | 0.028 | |
| makeBoxplotControls | 0.016 | 0.000 | 0.017 | |
| makeBoxplotControlsPerPlate | 0.064 | 0.000 | 0.061 | |
| makeBoxplotControlsPerScreen | 0.032 | 0.000 | 0.034 | |
| makeBoxplotPerPlate | 0.032 | 0.000 | 0.031 | |
| makeBoxplotPerScreen | 0.016 | 0.000 | 0.015 | |
| multTestAdjust | 0.000 | 0.000 | 0.001 | |
| numCellQualControl | 0.016 | 0.000 | 0.017 | |
| orderGeneIDs | 0.024 | 0.000 | 0.026 | |
| percCellQualControl | 0.016 | 0.000 | 0.016 | |
| plotBar | 0.092 | 0.004 | 0.098 | |
| plotControlHisto | 0.044 | 0.000 | 0.045 | |
| plotControlHistoPerplate | 0.280 | 0.004 | 0.285 | |
| plotControlHistoPerscreen | 0.188 | 0.000 | 0.187 | |
| plotHisto | 0.020 | 0.000 | 0.018 | |
| plotHistoPerplate | 0.076 | 0.000 | 0.075 | |
| plotHistoPerscreen | 0.036 | 0.000 | 0.037 | |
| plotQQ | 0.024 | 0.004 | 0.026 | |
| plotQQperplate | 0.084 | 0.000 | 0.086 | |
| plotQQperscreen | 0.040 | 0.004 | 0.046 | |
| quantileNormalization | 0.020 | 0.000 | 0.019 | |
| replicatesCV | 0.048 | 0.000 | 0.048 | |
| replicatesSpearmancor | 0.02 | 0.00 | 0.02 | |
| rms | 0.004 | 0.000 | 0.002 | |
| rnaither | 7.932 | 0.036 | 7.981 | |
| saveDataset | 0.008 | 0.000 | 0.008 | |
| saveOldIntensityColumns | 0.000 | 0.000 | 0.002 | |
| savepValVec | 0.004 | 0.000 | 0.003 | |
| spatialDistrib | 0.224 | 0.000 | 0.226 | |
| spatialDistribHits | 0.236 | 0.004 | 0.241 | |
| subtractBackground | 0.000 | 0.000 | 0.003 | |
| sumChannels | 0.008 | 0.000 | 0.008 | |
| summarizeReps | 0.024 | 0.000 | 0.023 | |
| summarizeRepsNoFiltering | 0.020 | 0.000 | 0.022 | |
| trim | 0.000 | 0.000 | 0.002 | |
| varAdjust | 0.008 | 0.000 | 0.004 | |
| vennDiag | 0.044 | 0.000 | 0.046 | |
| volcanoPlot | 0.036 | 0.000 | 0.033 | |